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Crystal structure of the C-terminal domain of Escherichia coli lipoprotein BamC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YH5 PDB ENTRY 2YH5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 0.1 M sodium chloride, 0.1 M HEPES, pH 6.5, 1.6 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.46 50.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.85 α = 90 b = 78.85 β = 90 c = 52.9 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror 2011-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.98058 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.5 41.82 99.7 0.075 0.034 10.3 5.7 19576 19576 5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 100 0.378 0.176 3.2 5.6 2877
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2YH5 1.5 41.82 19576 18558 999 99.59 0.16195 0.16085 0.1581 0.18321 0.1817 RANDOM 27.966
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.06 0.03 0.06 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.535 r_dihedral_angle_4_deg 28.57 r_dihedral_angle_3_deg 16.433 r_dihedral_angle_1_deg 6.204 r_scangle_it 5.646 r_scbond_it 3.731 r_mcangle_it 2.673 r_mcbond_it 1.781 r_angle_refined_deg 1.596 r_chiral_restr 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.535 r_dihedral_angle_4_deg 28.57 r_dihedral_angle_3_deg 16.433 r_dihedral_angle_1_deg 6.204 r_scangle_it 5.646 r_scbond_it 3.731 r_mcangle_it 2.673 r_mcbond_it 1.781 r_angle_refined_deg 1.596 r_chiral_restr 0.136 r_gen_planes_refined 0.017 r_bond_refined_d 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 901 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 2
Software Software Software Name Purpose Mx data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling